dsb

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## Advance use error

5

Hi, I am using the latest version 1.0.3 When using argument scsle.factor = "mean_subtract I get the following error: [1] "correcting ambient protein background noise" [1] "fitting models to each...

Sogand65

ValueError (ill-defined empirical covariance)

2

Thank you for the wonderful package to analyse CITE-seq. I'm having an error while running dsb and below is the code and error message: `pt.pp.dsb(filtered, raw, empty_counts_range=(2, 3), random_state=1)` Having...

m21camby

Integrated multiple samples

7

Hi, Thanks for the excellent method for CITE-seq! I find the vignettes from "https://cran.r-project.org/web/packages/dsb/vignettes/end_to_end_workflow.html" only deal with one sample. If I have multiple samples (more than 3) CITE-seq data and...

Aaron-sqw

Hi DSB team, After DSB (steps 1 and 2) on a recent analyses, I am noticing a phenomenon for a subset of the cells present in the data: negative values...

diegoalexespi

How dsb used in subpopulation anntation.

4

Thanks for the good tool. When we annotate the cell subsets (level2 and level3), we usually need to re-perform the batch correction, dimensionality reduction, and clustering. In this case, do...

bioyanguo

Understanding background filtering in dsb normalization

1

Hi, Thank you for this great package. I wanted to get some advice/understanding on some areas mentioned in the vignette. In step 3 of the vignette where you do some...

Chiranjit1504

Hi, Here is my code. I keep running into `Error: std::bad_alloc` and am not able to resolve it. ``` library(dsb) library(ComplexHeatmap) library(ggplot2) library(pheatmap) library(scCustomize) library(Seurat) # scp [email protected]:/n/scratch/users/s/sak4832/Cite_seq_latest/majority_doublet_predictions.R . #...

smk5g5